The field of proteomics is important as a basic science - probing the biochemical basis of life - and for a myriad of clinical applications, ranging from drug discovery to assays for gene expression. Proteomics is currently limited by a lack of high-throughput methods to identify proteins in complex samples. A novel combination of the electrowetting-on-dielectric (EWOD) fluid handling technique and matrix assisted laser desorption ionization mass spectrometry (MALDI-MS) is proposed in response to this challenge. This work will be pursued with two primary goals: (1) to establish the merits of EWOD-based arrays of protein samples for high-throughput analysis with MALDI-MS, and (2) to enhance the functionality of this technology by demonstrating a variety of in-line processing steps, including sample decontamination and proteolytic digestion. If successful, this will be a major advance over existing technologies, which do not have the capacity to combine high-throughput arrays with sample processing.